rs7676731

Variant names:

• chr4-108301296-G-A
• rs7676731
• ENST00000732953.1:n.594-3345G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000732953.1(LEF1-AS1):​n.594-3345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,960 control chromosomes in the GnomAD database, including 28,745 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (28745 hom., cov: 32)
• Consequence: LEF1-AS1 ENST00000732953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 1 publications found

Genes affected

LEF1-AS1 (HGNC:40339): (LEF1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LEF1-AS1	ENST00000732953.1	n.594-3345G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89515 AN: 151842 Hom.: 28726 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.623

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.589 AC: 89558 AN: 151960 Hom.: 28745 Cov.: 32 AF XY: 0.595 AC XY: 44172 AN XY: 74270

African (AFR) AF: 0.320 AC: 13237 AN: 41414

American (AMR) AF: 0.712 AC: 10868 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4277 AN: 5170

South Asian (SAS) AF: 0.687 AC: 3304 AN: 4806

European-Finnish (FIN) AF: 0.705 AC: 7436 AN: 10548

Middle Eastern (MID) AF: 0.693 AC: 201 AN: 290

European-Non Finnish (NFE) AF: 0.673 AC: 45747 AN: 67970

Other (OTH) AF: 0.628 AC: 1326 AN: 2112

Alfa AF: 0.603 Hom.: 3762

Bravo AF: 0.583

Asia WGS AF: 0.763 AC: 2636 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.55
PhyloP100		-0.089

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7676731; hg19: chr4-109222452;